Deubiquitinating enzymes—the importance of driving in reverse along the ubiquitin–proteasome pathway

Abstract

Ubiquitination of proteins is now recognized to target proteins for degradation by the proteasome and for internalization into the lysosomal system, as well as to modify functions of some target proteins. Although much progress has been made in characterizing enzymes that link ubiquitin to proteins, our understanding of deubiquitinating enzymes is less developed. These enzymes are involved in processing the products of ubiquitin genes which all encode fusion proteins, in negatively regulating the functions of ubiquitination (editing), in regenerating free ubiquitin after proteins have been targeted to the proteasome or lysosome (recycling) and in salvaging ubiquitin from possible adducts formed with small molecule nucleophiles in the cell. A large number of genes encode deubiquitinating enzymes suggesting that many have highly specific and regulated functions. Indeed, recent findings provide strong support for the concept that ubiquitination is regulated by both specific pathways of ubiquitination and deubiquitination. Interestingly, many of these enzymes are localized to subcellular structures or to molecular complexes. These localizations play important roles in determining specificity of function and can have major influences on their catalytic activities. Future studies, particularly aimed at characterizing the interacting partners and potential substrates in these complexes as well as at determining the effects of loss of function of specific deubiquitinating enzymes will rapidly advance our understanding of the important roles of these enzymes as biological regulators.

Introduction

The discovery and characterization of the ubiquitin system has been one of the most exciting developments in biology in the past two decades. During this period, our understanding of the covalent linking of ubiquitin via an isopeptide linkage to the ε-amino group of lysine residues on target proteins has evolved from that of an unusual post-translational modification of uncertain importance to one in which this modification is now recognized to control the steady-state levels of numerous key regulatory molecules in the cell and/or influence their localization and function. As all of these effects are related to the covalent linking of ubiquitin to proteins, much attention has been paid to characterizing the enzymes responsible for adding this moiety to proteins. However, analogous to the protein phosphorylation system where phosphatases play important regulatory roles, deubiquitinating enzymes probably play similarly important regulatory roles. In addition, ubiquitin has the unique feature of being encoded in the genome as a fusion protein either to itself or to a ribosomal subunit and so some deubiquitinating enzymes have the function of cleaving these linear ubiquitin fusions precisely into the monomeric proteins. Although deubiquitinating enzymes have been recognized for some time, they are less well characterized compared to those involved in ubiquitination. In this review, I will summarize basic information about the major families of deubiquitinating enzymes, emphasize recent advances and illustrate some of the questions that remain to be answered.